Multiple sequence alignment - TraesCS7A01G322700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G322700 chr7A 100.000 2696 0 0 1 2696 468299666 468302361 0.000000e+00 4979
1 TraesCS7A01G322700 chr7A 92.610 1881 110 10 819 2696 668181213 668183067 0.000000e+00 2676
2 TraesCS7A01G322700 chr7A 94.094 1761 92 5 938 2696 537035383 537037133 0.000000e+00 2665
3 TraesCS7A01G322700 chr7A 83.743 1341 181 21 1375 2696 477199466 477200788 0.000000e+00 1234
4 TraesCS7A01G322700 chr3B 98.480 2697 39 2 1 2696 292164226 292161531 0.000000e+00 4752
5 TraesCS7A01G322700 chr2A 92.181 1880 113 12 819 2696 629533071 629534918 0.000000e+00 2627
6 TraesCS7A01G322700 chr2A 88.553 1520 136 16 1178 2696 5903178 5904660 0.000000e+00 1808
7 TraesCS7A01G322700 chr5B 94.261 1638 88 4 1062 2696 652564023 652565657 0.000000e+00 2499
8 TraesCS7A01G322700 chr5B 88.845 1533 134 24 1180 2696 63985454 63983943 0.000000e+00 1849
9 TraesCS7A01G322700 chr5B 95.956 816 33 0 1 816 534307965 534308780 0.000000e+00 1325
10 TraesCS7A01G322700 chr5B 97.312 186 5 0 819 1004 652563835 652564020 1.560000e-82 316
11 TraesCS7A01G322700 chr3A 94.644 1587 72 4 819 2402 672321198 672322774 0.000000e+00 2447
12 TraesCS7A01G322700 chr3A 88.454 1533 127 21 1178 2696 732712057 732710561 0.000000e+00 1805
13 TraesCS7A01G322700 chr3A 93.276 818 38 8 1 818 686550688 686549888 0.000000e+00 1190
14 TraesCS7A01G322700 chr3A 93.318 449 24 2 370 818 11684699 11684257 0.000000e+00 658
15 TraesCS7A01G322700 chr3A 93.056 432 24 2 387 818 11710064 11709639 6.340000e-176 627
16 TraesCS7A01G322700 chr3A 91.582 297 14 6 1 297 11685337 11685052 1.500000e-107 399
17 TraesCS7A01G322700 chr4A 88.128 1533 131 22 1178 2696 208835994 208834499 0.000000e+00 1775
18 TraesCS7A01G322700 chr4A 91.606 822 43 7 1 822 614874402 614873607 0.000000e+00 1112
19 TraesCS7A01G322700 chr6A 97.924 819 16 1 1 818 29294864 29294046 0.000000e+00 1417
20 TraesCS7A01G322700 chr6A 92.929 396 24 3 395 788 100302510 100302117 8.370000e-160 573
21 TraesCS7A01G322700 chr6A 92.216 334 15 3 1 334 100302837 100302515 1.890000e-126 462
22 TraesCS7A01G322700 chr7B 95.610 820 30 5 1 818 728657340 728658155 0.000000e+00 1310
23 TraesCS7A01G322700 chr7B 94.238 833 43 5 1 829 29703037 29703868 0.000000e+00 1267
24 TraesCS7A01G322700 chr7B 86.078 668 86 3 1126 1791 705031703 705032365 0.000000e+00 712
25 TraesCS7A01G322700 chr7B 89.474 532 49 5 87 611 680641293 680641824 0.000000e+00 665
26 TraesCS7A01G322700 chr7B 89.504 524 48 5 95 611 680634013 680634536 0.000000e+00 656
27 TraesCS7A01G322700 chr7B 87.810 525 56 6 95 611 680627234 680627758 2.300000e-170 608
28 TraesCS7A01G322700 chr7D 83.217 1293 166 26 1386 2659 123837194 123835934 0.000000e+00 1138
29 TraesCS7A01G322700 chr5A 85.097 718 96 5 1126 1841 701459798 701460506 0.000000e+00 723
30 TraesCS7A01G322700 chr1D 85.944 683 81 8 1138 1816 58919458 58918787 0.000000e+00 715
31 TraesCS7A01G322700 chr5D 85.028 708 92 8 1138 1842 441693449 441692753 0.000000e+00 708
32 TraesCS7A01G322700 chr4B 91.045 536 30 6 91 611 251666333 251666865 0.000000e+00 708
33 TraesCS7A01G322700 chr3D 87.952 498 30 17 1 483 315763841 315763359 6.520000e-156 560
34 TraesCS7A01G322700 chr3D 82.282 333 36 16 820 1134 48065219 48065546 1.590000e-67 267
35 TraesCS7A01G322700 chr3D 82.143 336 37 16 820 1137 48086495 48086165 1.590000e-67 267
36 TraesCS7A01G322700 chr3D 82.036 334 37 15 820 1134 593594744 593594415 2.060000e-66 263
37 TraesCS7A01G322700 chr6D 82.440 336 36 15 820 1137 464449774 464449444 3.420000e-69 272


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G322700 chr7A 468299666 468302361 2695 False 4979.0 4979 100.0000 1 2696 1 chr7A.!!$F1 2695
1 TraesCS7A01G322700 chr7A 668181213 668183067 1854 False 2676.0 2676 92.6100 819 2696 1 chr7A.!!$F4 1877
2 TraesCS7A01G322700 chr7A 537035383 537037133 1750 False 2665.0 2665 94.0940 938 2696 1 chr7A.!!$F3 1758
3 TraesCS7A01G322700 chr7A 477199466 477200788 1322 False 1234.0 1234 83.7430 1375 2696 1 chr7A.!!$F2 1321
4 TraesCS7A01G322700 chr3B 292161531 292164226 2695 True 4752.0 4752 98.4800 1 2696 1 chr3B.!!$R1 2695
5 TraesCS7A01G322700 chr2A 629533071 629534918 1847 False 2627.0 2627 92.1810 819 2696 1 chr2A.!!$F2 1877
6 TraesCS7A01G322700 chr2A 5903178 5904660 1482 False 1808.0 1808 88.5530 1178 2696 1 chr2A.!!$F1 1518
7 TraesCS7A01G322700 chr5B 63983943 63985454 1511 True 1849.0 1849 88.8450 1180 2696 1 chr5B.!!$R1 1516
8 TraesCS7A01G322700 chr5B 652563835 652565657 1822 False 1407.5 2499 95.7865 819 2696 2 chr5B.!!$F2 1877
9 TraesCS7A01G322700 chr5B 534307965 534308780 815 False 1325.0 1325 95.9560 1 816 1 chr5B.!!$F1 815
10 TraesCS7A01G322700 chr3A 672321198 672322774 1576 False 2447.0 2447 94.6440 819 2402 1 chr3A.!!$F1 1583
11 TraesCS7A01G322700 chr3A 732710561 732712057 1496 True 1805.0 1805 88.4540 1178 2696 1 chr3A.!!$R3 1518
12 TraesCS7A01G322700 chr3A 686549888 686550688 800 True 1190.0 1190 93.2760 1 818 1 chr3A.!!$R2 817
13 TraesCS7A01G322700 chr3A 11684257 11685337 1080 True 528.5 658 92.4500 1 818 2 chr3A.!!$R4 817
14 TraesCS7A01G322700 chr4A 208834499 208835994 1495 True 1775.0 1775 88.1280 1178 2696 1 chr4A.!!$R1 1518
15 TraesCS7A01G322700 chr4A 614873607 614874402 795 True 1112.0 1112 91.6060 1 822 1 chr4A.!!$R2 821
16 TraesCS7A01G322700 chr6A 29294046 29294864 818 True 1417.0 1417 97.9240 1 818 1 chr6A.!!$R1 817
17 TraesCS7A01G322700 chr6A 100302117 100302837 720 True 517.5 573 92.5725 1 788 2 chr6A.!!$R2 787
18 TraesCS7A01G322700 chr7B 728657340 728658155 815 False 1310.0 1310 95.6100 1 818 1 chr7B.!!$F6 817
19 TraesCS7A01G322700 chr7B 29703037 29703868 831 False 1267.0 1267 94.2380 1 829 1 chr7B.!!$F1 828
20 TraesCS7A01G322700 chr7B 705031703 705032365 662 False 712.0 712 86.0780 1126 1791 1 chr7B.!!$F5 665
21 TraesCS7A01G322700 chr7B 680641293 680641824 531 False 665.0 665 89.4740 87 611 1 chr7B.!!$F4 524
22 TraesCS7A01G322700 chr7B 680634013 680634536 523 False 656.0 656 89.5040 95 611 1 chr7B.!!$F3 516
23 TraesCS7A01G322700 chr7B 680627234 680627758 524 False 608.0 608 87.8100 95 611 1 chr7B.!!$F2 516
24 TraesCS7A01G322700 chr7D 123835934 123837194 1260 True 1138.0 1138 83.2170 1386 2659 1 chr7D.!!$R1 1273
25 TraesCS7A01G322700 chr5A 701459798 701460506 708 False 723.0 723 85.0970 1126 1841 1 chr5A.!!$F1 715
26 TraesCS7A01G322700 chr1D 58918787 58919458 671 True 715.0 715 85.9440 1138 1816 1 chr1D.!!$R1 678
27 TraesCS7A01G322700 chr5D 441692753 441693449 696 True 708.0 708 85.0280 1138 1842 1 chr5D.!!$R1 704
28 TraesCS7A01G322700 chr4B 251666333 251666865 532 False 708.0 708 91.0450 91 611 1 chr4B.!!$F1 520

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
483 795 0.830648 TGTAGTGGAGGTAGCATGGC 59.169 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2528 3.521126 AGATATCAAGTCAGCAACCCAGT 59.479 43.478 5.32 0.0 0.0 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 648 5.105023 TCCATCTCCTTCTCTGAATTCTGTG 60.105 44.000 7.05 7.48 0.0 3.66
411 723 7.808279 TCTGTTTTCCTAATCTCCTCCTTTA 57.192 36.000 0.00 0.00 0.0 1.85
483 795 0.830648 TGTAGTGGAGGTAGCATGGC 59.169 55.000 0.00 0.00 0.0 4.40
518 830 2.020720 TGGTTGTTGCTCGTGTGATTT 58.979 42.857 0.00 0.00 0.0 2.17
985 1302 9.739276 ACTAAAGATTGATTCATGTTGTTCCTA 57.261 29.630 0.00 0.00 0.0 2.94
2067 2416 7.497909 AGGTTGTAATGTATGGTTTCTAATCCG 59.502 37.037 0.00 0.00 0.0 4.18
2130 2479 9.085645 TGATTTTTAGGAGAACGATATAGGCTA 57.914 33.333 0.00 0.00 0.0 3.93
2521 2883 5.120519 CACAAGAGAGAGCATTTGAAGAGAC 59.879 44.000 0.00 0.00 0.0 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 648 3.656559 TCTGAACCTAAAACACCTACGC 58.343 45.455 0.00 0.0 0.00 4.42
518 830 6.769822 GGCTTCTTCTCATTATCATCTTCCAA 59.230 38.462 0.00 0.0 0.00 3.53
722 1039 6.803366 AAAACTAGGATACAGGGATACGTT 57.197 37.500 0.00 0.0 41.41 3.99
985 1302 9.539825 CATAGATAGCATTGTCTAAAAGAGTGT 57.460 33.333 0.00 0.0 31.82 3.55
1128 1445 4.965119 ACTTCTCAGTTTTGCGTTTTCT 57.035 36.364 0.00 0.0 0.00 2.52
1672 1994 3.988976 TGCTGATGAAGTAAAGCTCCT 57.011 42.857 0.00 0.0 36.60 3.69
2067 2416 9.090692 CAAATCAACAAATCATACTGGATTTCC 57.909 33.333 0.00 0.0 43.66 3.13
2114 2463 9.182933 CAAACTAAACTAGCCTATATCGTTCTC 57.817 37.037 0.00 0.0 0.00 2.87
2178 2528 3.521126 AGATATCAAGTCAGCAACCCAGT 59.479 43.478 5.32 0.0 0.00 4.00
2521 2883 1.986378 CTTCGTGTTGCTTCCTCTACG 59.014 52.381 0.00 0.0 0.00 3.51


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.